The following bash command can be used to extract the compressed sequence and pipe it to the script (solexa2sanger_fq.py).

+

Pipes are a feature of the command line that enable the stdout output of a program or command to be directed to the stdin input of another command or program. For example, the following shell command can be used to extract the compressed sequence and pipe it to the script (solexa2sanger_fq.py).

<bash>

<bash>

Line 25:

Line 25:

This will write the sequence in Sanger FASTQ format to stdout - in this case the screen.

This will write the sequence in Sanger FASTQ format to stdout - in this case the screen.

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You might can also use it like this, where the python script is fed its data from an input file, and the output which would have been printed to screen is instead sent to an output file:

+

Redirection is similar to using pipes, but instead of directing the output of one program to the input of another, redirection redirects the contents of a file to a program's stdin, and/or the output of a program's stdout to a file. In this example, the python script is fed its data redirected from an input file, and the output which would have been printed to screen is instead redirected to an output file:

<bash>

<bash>

Line 31:

Line 31:

</bash>

</bash>

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Redirection can also be used to redirect a program or command's stderr to a file. Further examples of using redirection can be found [http://tldp.org/HOWTO/Bash-Prog-Intro-HOWTO-3.html here].

[[Category:Cookbook]]

[[Category:Cookbook]]

Revision as of 08:17, 9 June 2009

Problem

There are many circumstances when reading data from a Unix pipe is preferable to reading data from a file. One example is reading sequences from a compressed file, which is often preferable to uncompressing the file and then reading from it.

You can also use pipes at the Windows command line, but this isn't quite as flexible.

Solution

This example script reads a Solexa/Illumina FASTQ from stdin, converts the data to Sanger FASTQ (using PHRED scores) and writes it to stdout.

Pipes are a feature of the command line that enable the stdout output of a program or command to be directed to the stdin input of another command or program. For example, the following shell command can be used to extract the compressed sequence and pipe it to the script (solexa2sanger_fq.py).

gunzip-c some_solexa.fastq.gz | python solexa2sanger_fq.py

This will write the sequence in Sanger FASTQ format to stdout - in this case the screen.

Redirection is similar to using pipes, but instead of directing the output of one program to the input of another, redirection redirects the contents of a file to a program's stdin, and/or the output of a program's stdout to a file. In this example, the python script is fed its data redirected from an input file, and the output which would have been printed to screen is instead redirected to an output file:

python solexa2sanger_fq.py < some_solexa.fastq > some_phred.fastq

Redirection can also be used to redirect a program or command's stderr to a file. Further examples of using redirection can be found here.